Visualization of SexFindR Steps
Shannon EK Joslin
2023-02-24
Step 1: difcover
Step 2: SNPdensity
Female Reference Genome
Male Reference Genome
Step 2: GWAS & Fst
Female Reference Genome
PCA
All individuals
## [1] 5.554972 11.049963 16.493342 21.834145 27.027838 32.101151
## [7] 37.155872 42.182614 47.156312 52.104758 57.029665 61.904487
## [13] 66.748277 71.564689 76.345953 81.108673 85.862467 90.585923
## [19] 95.302720 100.000000## [1] "full dataset - female ref"
## [1] "full dataset - female ref - zoom"
## [1] "full dataset - female ref"## quartz_off_screen
## 2# grab outliers
pca_outliers_f <- pca_f %>% filter(PC1 > 0.25 | PC2 < -0.1 | PC2 > 0.25)
print(pca_outliers_f$ind)## [1] "RX41_2_M_F11_AAGGACAC.sort-n.fixmate-m.sort.markdup-r"
## [2] "RX47_1_F_G08_ATAGCGAC.sort-n.fixmate-m.sort.markdup-r"
## [3] "RX59_2_M_H11_GATGAATC.sort-n.fixmate-m.sort.markdup-r"
## [4] "RX68_2_M_G12_CACCTTAC.sort-n.fixmate-m.sort.markdup-r"No Outliers
## [1] 5.346634 10.560970 15.757442 20.890464 26.003575 31.102359
## [7] 36.170534 41.207914 46.224175 51.221735 56.191477 61.135634
## [13] 66.053229 70.953426 75.831527 80.700464 85.564656 90.389354
## [19] 95.199957 100.000000## [1] "no outliers - female ref"
## [1] "no outliers - female ref - zoom"
## [1] "no outliers - female ref"
## [1] "female ref\n row1=full dataset, row2=filtered"## quartz_off_screen
## 2GWAS
All Individuals
No Outliers
Fst
All Individuals
## [1] 0.0737052## [1] 0.243856##
## lg01 lg02 lg03 lg04 lg05 lg06
## 83 90 108 82 51 89
## lg07 lg08 lg09 lg10 lg11 lg12
## 79 99 129 96 145 89
## lg13 lg14 lg15 lg16 lg17 lg18
## 91 141 98 32 98 95
## lg19 lg20 lg21 lg22 lg23 lg24
## 118 39 59 106 138 38
## lg25 lg26 scaffold_101 scaffold_105 scaffold_107 scaffold_111
## 37 63 1 3 5 3
## scaffold_116 scaffold_122 scaffold_124 scaffold_127 scaffold_129 scaffold_130
## 4 3 8 3 4 3
## scaffold_131 scaffold_132 scaffold_133 scaffold_134 scaffold_137 scaffold_138
## 1 6 20 3 2 2
## scaffold_139 scaffold_143 scaffold_146 scaffold_149 scaffold_152 scaffold_154
## 4 1 6 3 7 1
## scaffold_156 scaffold_159 scaffold_160 scaffold_166 scaffold_170 scaffold_172
## 4 2 10 5 6 1
## scaffold_181 scaffold_184 scaffold_185 scaffold_186 scaffold_187 scaffold_192
## 1 2 1 2 1 1
## scaffold_194 scaffold_195 scaffold_199 scaffold_201 scaffold_203 scaffold_204
## 5 3 2 1 3 1
## scaffold_205 scaffold_208 scaffold_210 scaffold_214 scaffold_218 scaffold_221
## 1 2 2 2 3 1
## scaffold_223 scaffold_224 scaffold_225 scaffold_226 scaffold_227 scaffold_228
## 3 1 3 1 1 3
## scaffold_229 scaffold_231 scaffold_232 scaffold_234 scaffold_235 scaffold_236
## 2 1 1 1 1 3
## scaffold_241 scaffold_243 scaffold_250 scaffold_251 scaffold_256 scaffold_257
## 2 4 4 2 2 1
## scaffold_258 scaffold_260 scaffold_263 scaffold_264 scaffold_266 scaffold_27
## 1 5 1 2 1 25
## scaffold_270 scaffold_273 scaffold_276 scaffold_280 scaffold_284 scaffold_287
## 1 1 1 2 1 1
## scaffold_289 scaffold_290 scaffold_292 scaffold_293 scaffold_294 scaffold_295
## 1 1 1 1 1 2
## scaffold_296 scaffold_297 scaffold_30 scaffold_300 scaffold_306 scaffold_309
## 1 3 24 2 1 1
## scaffold_31 scaffold_311 scaffold_312 scaffold_318 scaffold_321 scaffold_323
## 28 1 3 1 1 1
## scaffold_325 scaffold_326 scaffold_329 scaffold_330 scaffold_332 scaffold_333
## 1 1 2 1 1 2
## scaffold_335 scaffold_338 scaffold_339 scaffold_350 scaffold_353 scaffold_354
## 2 3 1 1 2 1
## scaffold_356 scaffold_369 scaffold_380 scaffold_381 scaffold_383 scaffold_386
## 1 4 1 1 1 1
## scaffold_389 scaffold_391 scaffold_409 scaffold_414 scaffold_42 scaffold_421
## 2 1 1 1 20 2
## scaffold_425 scaffold_426 scaffold_431 scaffold_434 scaffold_437 scaffold_438
## 1 1 2 1 1 1
## scaffold_443 scaffold_446 scaffold_450 scaffold_468 scaffold_472 scaffold_474
## 2 1 1 1 1 1
## scaffold_477 scaffold_478 scaffold_48 scaffold_480 scaffold_483 scaffold_491
## 1 1 2 1 1 1
## scaffold_495 scaffold_499 scaffold_503 scaffold_51 scaffold_512 scaffold_52
## 1 1 1 1 1 4
## scaffold_55 scaffold_60 scaffold_61 scaffold_62 scaffold_64 scaffold_65
## 2 1 11 5 3 4
## scaffold_84 scaffold_88 scaffold_89 scaffold_90 scaffold_91 scaffold_94
## 8 2 4 1 1 1
## scaffold_96
## 6## 95% 99%
## 0.0737052 0.2438305## [1] 0.0182133
No Outliers
## [1] 0.118254## [1] 0.193863##
## lg01 lg02 lg03 lg04 lg05 lg06
## 1 1 1 4 1 2
## lg07 lg08 lg09 lg10 lg11 lg12
## 1 2 1 2 2 2
## lg13 lg14 lg15 lg16 lg17 lg18
## 1 2 1 1 3 3
## lg19 lg20 lg21 lg22 lg23 lg26
## 4 2 1 2 1 1
## scaffold_204 scaffold_225 scaffold_263 scaffold_27 scaffold_297 scaffold_357
## 1 1 1 1 1 1
## scaffold_42
## 1## 95% 99%
## 0.117942 0.193146## [1] 0.03776015
## [1] 0.118254## [1] 0.193863##
## lg01 lg02 lg03 lg04 lg05 lg06
## 1 1 1 4 1 2
## lg07 lg08 lg09 lg10 lg11 lg12
## 1 2 1 2 2 2
## lg13 lg14 lg15 lg16 lg17 lg18
## 1 2 1 1 3 3
## lg19 lg20 lg21 lg22 lg23 lg26
## 4 2 1 2 1 1
## scaffold_204 scaffold_225 scaffold_263 scaffold_27 scaffold_297 scaffold_357
## 1 1 1 1 1 1
## scaffold_42
## 1## 95% 99%
## 0.117942 0.193146## [1] 0.03776015
Male Reference Genome
PCA
All Individuals
## [1] 5.608953 11.067687 16.446146 21.680707 26.857506 31.981802
## [7] 37.071635 42.133003 47.140576 52.124343 57.057546 61.969341
## [13] 66.819038 71.647512 76.427544 81.172927 85.905439 90.617190
## [19] 95.315377 100.000000## [1] "full dataset - male ref"
## [1] "full dataset - male ref - zoom"
## quartz_off_screen
## 2# grab outliers
pca_outliers_m <- pca_m %>% filter(PC1 < -0.25 | PC2 < -0.25)
head(pca_outliers_m$ind)## [1] "RX41_2_M_F11_AAGGACAC.sort-n.fixmate-m.sort.markdup-r"
## [2] "RX59_2_M_H11_GATGAATC.sort-n.fixmate-m.sort.markdup-r"
## [3] "RX68_2_M_G12_CACCTTAC.sort-n.fixmate-m.sort.markdup-r"No Outliers
## [1] 5.321484 10.552065 15.736116 20.897567 26.001281 31.085564
## [7] 36.147891 41.190007 46.218987 51.209520 56.179934 61.125177
## [13] 66.067067 70.968994 75.845061 80.715432 85.570783 90.404499
## [19] 95.208129 100.000000## [1] 5.321484 10.552065 15.736116 20.897567 26.001281 31.085564
## [7] 36.147891 41.190007 46.218987 51.209520 56.179934 61.125177
## [13] 66.067067 70.968994 75.845061 80.715432 85.570783 90.404499
## [19] 95.208129 100.000000## [1] "No Outliers - MaleRef"
## [1] "No Outliers - MaleRef - Zoom"
## [1] "no outliers - female ref"
## [1] "male ref\n row1=full dataset, row2=filtered"## quartz_off_screen
## 2GWAS
All Individuals
No Outlier
Fst
All Individuals
## [1] 0.074878## [1] 0.248619##
## lg01 lg02 lg03 lg04 lg05 lg06
## 95 70 126 86 73 107
## lg07 lg08 lg09 lg10 lg11 lg12
## 68 101 106 59 118 76
## lg13 lg14 lg15 lg16 lg17 lg18
## 73 120 67 32 61 93
## lg19 lg20 lg21 lg22 lg23 lg24
## 102 43 53 95 112 14
## lg25 lg26 scaffold_106 scaffold_107 scaffold_111 scaffold_113
## 27 57 2 3 1 8
## scaffold_122 scaffold_129 scaffold_133 scaffold_134 scaffold_136 scaffold_137
## 3 2 1 3 1 1
## scaffold_138 scaffold_141 scaffold_142 scaffold_143 scaffold_145 scaffold_150
## 2 3 2 4 1 1
## scaffold_152 scaffold_154 scaffold_155 scaffold_156 scaffold_157 scaffold_166
## 6 1 1 2 1 4
## scaffold_169 scaffold_170 scaffold_171 scaffold_179 scaffold_182 scaffold_183
## 4 4 3 2 7 2
## scaffold_184 scaffold_185 scaffold_186 scaffold_194 scaffold_196 scaffold_20
## 2 1 9 4 1 13
## scaffold_202 scaffold_203 scaffold_204 scaffold_206 scaffold_207 scaffold_209
## 1 1 3 2 1 1
## scaffold_210 scaffold_212 scaffold_215 scaffold_222 scaffold_224 scaffold_227
## 2 1 1 2 2 3
## scaffold_228 scaffold_232 scaffold_233 scaffold_235 scaffold_236 scaffold_242
## 1 3 1 2 4 5
## scaffold_243 scaffold_248 scaffold_251 scaffold_256 scaffold_258 scaffold_260
## 2 1 1 3 1 3
## scaffold_262 scaffold_266 scaffold_28 scaffold_280 scaffold_282 scaffold_285
## 3 1 16 4 2 1
## scaffold_290 scaffold_291 scaffold_300 scaffold_301 scaffold_312 scaffold_321
## 3 1 2 1 1 1
## scaffold_322 scaffold_323 scaffold_324 scaffold_325 scaffold_330 scaffold_344
## 2 1 1 1 1 1
## scaffold_350 scaffold_353 scaffold_355 scaffold_357 scaffold_359 scaffold_364
## 1 2 4 4 2 1
## scaffold_365 scaffold_368 scaffold_370 scaffold_371 scaffold_374 scaffold_380
## 1 1 1 1 2 2
## scaffold_386 scaffold_413 scaffold_427 scaffold_429 scaffold_435 scaffold_441
## 5 2 2 1 3 2
## scaffold_444 scaffold_45 scaffold_451 scaffold_457 scaffold_458 scaffold_462
## 1 3 2 1 2 1
## scaffold_465 scaffold_467 scaffold_470 scaffold_479 scaffold_49 scaffold_493
## 1 1 4 2 5 3
## scaffold_495 scaffold_497 scaffold_498 scaffold_50 scaffold_511 scaffold_512
## 2 1 3 13 2 2
## scaffold_54 scaffold_547 scaffold_548 scaffold_552 scaffold_554 scaffold_557
## 2 1 1 2 1 1
## scaffold_57 scaffold_573 scaffold_579 scaffold_584 scaffold_595 scaffold_601
## 3 1 1 1 1 2
## scaffold_609 scaffold_61 scaffold_613 scaffold_616 scaffold_617 scaffold_622
## 2 2 1 2 1 2
## scaffold_623 scaffold_634 scaffold_637 scaffold_638 scaffold_639 scaffold_643
## 1 1 1 1 2 1
## scaffold_653 scaffold_661 scaffold_663 scaffold_670 scaffold_671 scaffold_674
## 3 1 2 1 1 1
## scaffold_676 scaffold_68 scaffold_680 scaffold_683 scaffold_685 scaffold_686
## 1 6 1 1 2 1
## scaffold_690 scaffold_693 scaffold_695 scaffold_705 scaffold_77 scaffold_81
## 1 1 2 1 3 3
## scaffold_82 scaffold_85 scaffold_89 scaffold_9 scaffold_90 scaffold_92
## 1 3 1 70 5 2
## scaffold_98
## 2## 95% 99%
## 0.074878 0.248619## [1] 0.01838211
No Outlier
## [1] 0.120286## [1] 0.186137##
## lg01 lg02 lg03 lg04 lg05 lg06
## 2 1 1 5 1 3
## lg08 lg09 lg10 lg11 lg12 lg15
## 1 1 4 1 3 1
## lg17 lg18 lg19 lg20 lg21 lg22
## 1 2 4 1 1 1
## lg24 lg26 scaffold_184 scaffold_20 scaffold_206 scaffold_226
## 1 3 1 1 1 1
## scaffold_243 scaffold_458 scaffold_622 scaffold_682
## 1 1 1 1## 95% 99%
## 0.1201978 0.1835650## [1] 0.03747152
## [1] 0.120286## [1] 0.186137##
## lg01 lg02 lg03 lg04 lg05 lg06
## 2 1 1 5 1 3
## lg08 lg09 lg10 lg11 lg12 lg15
## 1 1 4 1 3 1
## lg17 lg18 lg19 lg20 lg21 lg22
## 1 2 4 1 1 1
## lg24 lg26 scaffold_184 scaffold_20 scaffold_206 scaffold_226
## 1 3 1 1 1 1
## scaffold_243 scaffold_458 scaffold_622 scaffold_682
## 1 1 1 1## 95% 99%
## 0.1201978 0.1835650## [1] 0.03747152